Define your glossary terms under the glossary menu item in the administration interface. The title of the page should be the term. The body content should be the definition.

Creates a main Glossary page (example "Glossary") with no body content, if you so wish. If you do not create this page then your terms will still be highlighted, but without a central listing page of all your terms.

In the plugin's dashboard preferences, enter the main Glossary page's id (optional as above)

There are a handful of other optional preferences available in the dashboard.

Note: You must have a call to wp_head() in your template in order for the Tooltip js and css to work properly. If your theme does not support them you will need to link to these files manually in your theme (not recommended).